Metabolic and transcriptomic changes induced in Arabidopsis by the rhizobacterium Pseudomonas fluorescens SS101.

Abstract

Systemic resistance induced in plants by nonpathogenic rhizobacteria is typically effective against multiple pathogens. Here, we show that root-colonizing Pseudomonas fluorescens strain SS101 (Pf.SS101) enhanced resistance in Arabidopsis (Arabidopsis thaliana) against several bacterial pathogens, including Pseudomonas syringae pv tomato (Pst) and the insect pest Spodoptera exigua. Transcriptomic analysis and bioassays with specific Arabidopsis mutants revealed that, unlike many other rhizobacteria, the Pf.SS101-induced resistance response to Pst is dependent on salicylic acid signaling and not on jasmonic acid and ethylene signaling. Genome-wide transcriptomic and untargeted metabolomic analyses showed that in roots and leaves of Arabidopsis plants treated with Pf.SS101, approximately 1,910 genes and 50 metabolites were differentially regulated relative to untreated plants. Integration of both sets of "omics" data pointed to a prominent role of camalexin and glucosinolates in the Pf.SS101-induced resistance response. Subsequent bioassays with seven Arabidopsis mutants (myb51, cyp79B2cyp79B3, cyp81F2, pen2, cyp71A12, cyp71A13, and myb28myb29) disrupted in the biosynthesis pathways for these plant secondary metabolites showed that camalexin and glucosinolates are indeed required for the induction of Pst resistance by Pf.SS101. Also for the insect S. exigua, the indolic glucosinolates appeared to play a role in the Pf.SS101-induced resistance response. This study provides, to our knowledge for the first time, insight into the substantial biochemical and temporal transcriptional changes in Arabidopsis associated with the salicylic acid-dependent resistance response induced by specific rhizobacteria.

Effects of seed or root tip treatment of Arabidopsis wild-type with on resistance against different bacterial pathogens and the lepidopteran insect S. exigua. A, Disease incidence and population density on leaves of Arabidopsis grown in soil or in vitro. was applied 18 d (for soil assays; a–c) or 14 d (for in vitro assays; d–f) after seed or root tip treatment with . Symptoms were determined 5 to 7 d after inoculation. Values shown are means ± se of 20 to 30 plants. Experiments were performed at least twice, and representative results are shown. Asterisks indicate statistically significant differences from the control treatment (one-way ANOVA, P < 0.05). B, Disease incidence of Arabidopsis leaves after inoculation with , P. syringae pv maculicola, P. alisalensis, or P. viridiflava. Arabidopsis seeds were treated with and grown under in vitro conditions. Symptoms and population densities of these pathogens were determined 5 d after inoculation. Values shown are means ± se of four independent replicates of 10 plants each. Experiments were performed at least twice, and representative results are shown. Asterisks indicate statistically significant differences from the control treatment (one-way ANOVA, P < 0.05). C, Effects of on larval mortality of the lepidopteran insect S. exigua after 6 d of feeding. was inoculated on root tips of Arabidopsis seedlings grown in vitro. Values shown are back-transformed mortality means ± se based on 45 to 48 plates per treatment (two-way ). Experiments were performed twice with similar results. Asterisks indicate statistically significant differences from the control treatment (***P < 0.001). The inset shows a photograph of S. exigua (courtesy of Tibor Bukovinszky; www.bugsinthepicture.com).

Genome-wide transcriptional changes induced in Arabidopsis by . A, Total number of induced (red) and repressed (green) genes in roots or in leaves of Arabidopsis treated with . B and C, Venn diagrams displaying the overlap in differentially regulated Arabidopsis genes in roots (B) or in leaves (C) at 10, 14, and 18 with .

Untargeted ---based metabolic profiling of Arabidopsis treated with . A and B, - profiles of metabolites in the roots of Arabidopsis treated with (A) and mock-treated (control) Arabidopsis (B). C and D, - profiles of metabolites accumulated in the leaves of Arabidopsis treated with (C) and mock-treated (control) Arabidopsis (D). Prominent peaks that are significantly different (Student’s t test, P < 0.01) between the control and treatment are labeled with letters. The entire data set and statistical analyses are presented in Supplemental Table S7.